• Alternantia geitleri J. Schiller
• Alternantia quadriga Schiller
• Alternantia ramifera J. Schiller, 1954
• Alternantia serra Schiller
• Alternantia tabularis J. Schiller
• Bacillosiphon induratus Copeland, 1936 accepted as Bacularia indurata (Copeland) Frémy, 1949
• Bacularia caerulescens Borzì, 1905
• Bacularia coerulescens Borzì
• Bacularia gracilis Komárek, 1995
• Bacularia indurata (Copeland) Frémy, 1949
• Bacularia thermalis Frémy, 1949
• Bacularia vermicularis (Fedorov) Komárek & Anagnostidis, 1995
• Chroobacter vantieghemii Pringsheim, 1953 accepted as Synechococcus vantieghemii (Pringsheim) Bourrelly, 1970
• Cyanocatena bicudoi J.J. Ramírez, 1996
• Cyanocatena imperfecta (Cronberg & Weibull) van Joosten, 2006
• Cyanocatena planctonica Hindák, 1975
• Cyanodictyon balticum Cronberg
• Cyanodictyon endophyticum Pascher, 1914
• Cyanodictyon filiforme J. Komárková-Legnerová & G. Cronberg, 1994
• Cyanodictyon iac G. Cronberg & J. Komárek, 1994
• Cyanodictyon imperfectum Cronberg & Weibull, 1981
• Cyanodictyon intermedium van Joosten, 2006
• Cyanodictyon planctonicum B.A. Mayer, 1994
• Cyanodictyon reticulatum (Lemmermann) Geitler, 1925
• Cyanodictyon tropicale P.A.C. Senna, A. Delazari & C.L. Sant'Anna
• Cyanodictyon tubiforme Cronberg, 1988
• Cyanodictyon turfosum Lederer, 1995
• Cyanogranis basifixa Hindák, 1982
• Cyanogranis ferruginea (F. Wawrik) Hindák, 1982
• Cyanogranis irregularis van Joosten, 2006
• Cyanogranis libera Hindák
• Cyanonephron elegans van Joosten, 2006
• Cyanonephron styloides Hickel, 1985
• Cyanothamnos plancticus G. Cronberg, 1991
• Epigloeosphaera brasilica M.T.P. Azevedo et al.
• Epigloeosphaera filamentosa Komárek & Cronberg, 1998
• Epigloeosphaera glebulenta (Zalessky) J. Komárková-Legnerová, 1991
• Lauterbornia nidulans Pringsheim, 1968 accepted as Synechococcus nidulans (Pringsheim) Komárek, 1970
• Lemmermanniella flexa Hindák, 1985
• Lemmermanniella obesa M.T.P. Azevedo, C.A. Souza & M. Menezes, 1999
• Lemmermanniella pallida (Lemmermann) Geitler, 1942
• Lemmermanniella parva Hindák, 1985
• Lemmermanniella uliginosa Komárek & Komárek-Legnerová, 2007
• Lithococcus ramosus Ercegović, 1925
• Lithomyxa calcigena Howe, 1931
• Nostocopsis saprolithica Mädler †
• Rhabdoderma bellyeense Hortobágyi, 1944
• Rhabdoderma canillesiana Gonzalez
• Rhabdoderma cavanillesiana P. González, 1946
• Rhabdoderma compositum (G.M. Smith) Fedorov, 1967
• Rhabdoderma curtum (Setchell) Komárek & Anagnostidis, 1995
• Rhabdoderma gorskii Woloszynsky, 1917 accepted as Rhabdoderma lineare Schmidle & Lauterborn, 1900
• Rhabdoderma irregulare (Naumann) Geitler, 1925
• Rhabdoderma lineare Schmidle & Lauterborn, 1900
• Rhabdoderma minimum Lemmermann
• Rhabdoderma rubrum (Ålvik) Komárek & Anagnostidis, 1995
• Rhabdoderma salinum Tutin, 1940
• Rhabdoderma sanctipauli Azevedo et al.
• Rhabdoderma sancti-pauli M.T.P. Azevedo et al.
• Rhabdoderma sigmoideum Moore & Carter, 1923 accepted as Synechococcus sigmoideus (Moore & Carter) Komárek, 1970
• Rhabdoderma surchanense Ergasev, 1980
• Rhabdoderma tenuissimum J. Komárek & H. Kling, 1991
• Rhabdoderma transsylvanicum (Kol) Komárek & Anagnostidis, 1995
• Rhabdoderma vermiculare Fedorov, 1969 accepted as Bacularia vermicularis (Fedorov) Komárek & Anagnostidis, 1995
• Rhabdoderma vermiculare Fott, 1952
• Rhabdoderma zygnemicola Copeland, 1936
• Rhabdoderma zygnemicolum Copeland
• Rhabdogloea antarctica Fritsch, 1912
• Rhabdogloea brasilica M.T.P. Azevedo & L. Kovácik, 1996
• Rhabdogloea clathrata (W. West & G.S. West) J. Komárek
• Rhabdogloea elenkini (Roll) Komárek & Anagnostidis
• Rhabdogloea elenkinii (Roll) Komárek & Anagnostidis, 1995
• Rhabdogloea ellipsoidea Schröder, 1917
• Rhabdogloea gorskii (Woloszynska) Joosten
• Rhabdogloea hungarica (Kol) Hindák, 1984
• Rhabdogloea linearis (L. Geitler) J. Komárek, 1983
• Rhabdogloea minuta B. Hickel, 1991
• Rhabdogloea planctonica (E. Teiling) J. Komárek, 1983
• Rhabdogloea planktonica (Teiling) Komárek
• Rhabdogloea scenedesmoides (Nygaard) Komárek & Anagnostidis, 1995
• Rhabdogloea smithii (R. Chodat & F. Chodat) J. Komárek, 1983
• Rhabdogloea subtropica Hindák, 1984
• Rhabdogloea yucatanensis Komárek & Komárková-Legnerová
• Rhodostichus expansus Geitler & Pascher, 1931
• Rhodostichus fluminensis (Fritsch) Bourrelly, 1970 accepted as Cyanodermatium fluminense (Fritsch) Komárek & Anagnostidis, 1995
• Sphaerodictyon reticulatum (Lemmermann) Geitler, 1925 accepted as Cyanodictyon reticulatum (Lemmermann) Geitler, 1925
• Spirillopsis irregularis Naumann, 1921 accepted as Rhabdoderma irregulare (Naumann) Geitler, 1925
• Synechococcus aeruginosus Nägeli, 1849 accepted as Cyanothece aeruginosa (Nägeli) Komárek, 1976
• Synechococcus ambiguus Skuja, 1937
• Synechococcus amethystinus J.J. Copeland
• Synechococcus amphigranulatus (Copeland) Yoneda, 1943 accepted as Synechococcus bigranulatus Skuja, 1933
• Synechococcus arcuatus
• Synechococcus bacillaris Butcher, 1952 accepted as Cyanobium bacillare (Butcher) J. Komárek, J. Kopecký & V. Cepák, 1999
• Synechococcus bigranulatus Skuja, 1933
• Synechococcus bosshardii Skuja
• Synechococcus brunneolus Rabenhorst, 1863
• Synechococcus caldarius Okada, 1939
• Synechococcus capitatus A.E. Bailey-Watts & J. Komárek, 1991
• Synechococcus carcerarius R.E. Norris, 1967
• Synechococcus cedrorum Sauvageau, 1892 accepted as Cyanobacterium cedrorum (Sauvageau) Komárek, Kopecky & Cepák